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"Kaiser, Thomas"
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The computationally guided design of selective targeters of multiple proteins (STaMPs) as a new opportunity for small molecule drug discovery
Polypharmacology has long been an aspect of drug design for small molecules, and the multi-target pursuit has frequently behaved more akin to divine chance rather than controllable science. Targets unknown or once thought undesirable can often be revealed to be key points of intervention for the positive effects of a drug later in the development of a program or even after its approval. In this review, we look at historical examples of molecular pleiotropism and evaluate how new insights from computational systems biology and small molecule design can aid the rational design of Selective Targeters of Multiple Proteins (STaMPs).
Journal Article
Forage silica and water content control dental surface texture in guinea pigs and provide implications for dietary reconstruction
Recent studies have shown that phytoliths are softer than dental enamel but still act as abrasive agents. Thus, phytolith content should be reflected in dental wear. Because native phytoliths show lower indentation hardness than phytoliths extracted by dry ashing, we propose that the hydration state of plant tissue will also affect dental abrasion. To assess this, we performed a controlled feeding experiment with 36 adult guinea pigs, fed exclusively with three different natural forages: lucerne, timothy grass, and bamboo with distinct phytolith/silica contents (lucerne < grass < bamboo). Each forage was fed in fresh or dried state for 3 weeks. We then performed 3D surface texture analysis (3DST) on the upper fourth premolar. Generally, enamel surface roughness increased with higher forage phytolith/silica content. Additionally, fresh and dry grass feeders displayed differences in wear patterns, with those of fresh grass feeders being similar to fresh and dry lucerne (phytolith-poor) feeders, supporting previous reports that “fresh grass grazers” show less abrasion than unspecialized grazers. Our results demonstrate that not only phytolith content but also properties such as water content can significantly affect plant abrasiveness, even to such an extent that wear patterns characteristic for dietary traits (browser–grazer differences) become indistinguishable.
Journal Article
Dental microwear texture reflects dietary tendencies in extant Lepidosauria despite their limited use of oral food processing
Lepidosauria show a large diversity in dietary adaptations, both among extant and extinct tetrapods. Unlike mammals, Lepidosauria do not engage in sophisticated mastication of their food and most species have continuous tooth replacement, further reducing the wear of individual teeth. However, dietary tendency estimation of extinct lepidosaurs usually rely on tooth shape and body size, which allows only for broad distinction between faunivores and herbivores. Microscopic wear features on teeth have long been successfully applied to reconstruct the diet of mammals and allow for subtle discrimination of feeding strategies and food abrasiveness. Here, we present, to our knowledge, the first detailed analysis of dental microwear texture on extant lepidosaurs using a combination of 46 surface texture parameters to establish a framework for dietary tendency estimation of fossil reptilian taxa. We measured dental surface textures of 77 specimens, belonging to herbivorous, algaevorous, frugivorous, carnivorous, ovivorous, insectivorous, molluscivorous, as well as omnivorous species. Carnivores show low density and shallow depth of furrows, whereas frugivores are characterized by the highest density of furrows. Molluscivores show the deepest wear features and highest roughness, herbivores have lower surface roughness and shallower furrows compared to insectivores and omnivores, which overlap in all parameters. Our study shows that despite short food–tooth interaction, dental surface texture parameters enable discrimination of several feeding strategies in lepidosaurs. This result opens new research avenues to assess diet in a broad variety of extant and extinct non-mammalian taxa including dinosaurs and early synapsids.
Journal Article
Dietary Abrasiveness Is Associated with Variability of Microwear and Dental Surface Texture in Rabbits
Dental microwear and 3D surface texture analyses are useful in reconstructing herbivore diets, with scratches usually interpreted as indicators of grass dominated diets and pits as indicators of browse. We conducted feeding experiments with four groups of rabbits (Oryctolagus cuniculus) each fed a different uniform, pelleted diet (lucerne, lucerne & oats, grass & oats, grass). The lowest silica content was measured in the lucerne and the highest in the grass diet. After 25 weeks of exposure to the diets, dental castings were made of the rabbit's lower molars. Occlusal surfaces were then investigated using dental microwear and 3D areal surface texture analysis. In terms of traditional microwear, we found our hypothesis supported, as the grass group showed a high proportion of (long) \"scratches\" and the lucerne group a high proportion of \"pits\". Regardless of the uniform diets, variability of microwear and surface textures was higher when silica content was low. A high variability in microwear and texture analysis thus need not represent dietary diversity, but can also be related to a uniform, low-abrasion diet. The uniformity or variability of microwear/texture analysis results thus might represent varying degrees of abrasion and attrition rather than a variety of diet items per se.
Journal Article
Performance analysis of RFID localization based on dual-tag range sensors
Indoor localization based on radio technology has been a long-standing issue for the past two decades. In this paper, we study the localization problem by using dual-tag range sensors. We show that the localization problem can be converted into a constrained optimization problem. Based on this, we then derive the constrained Cramer–Rao lower bound (CCRB) for the localization system to characterize the limiting localization accuracy of the system. Two types of estimators are used to solve the localization problem. The first is the maximum likelihood estimator (MLE). The second is the
GlobalSearch
(
GS
) optimization algorithm. It is shown that the positioning performance of the MLE is close to the CCRB, but its computational burden is very heavy, making it only suitable for solving 2D localization problems. The
GS
algorithm gives good positioning performance for both 2D and 3D localization problems by closely following the trend of the CCRB, with the gap being within 3 dB in signal-to-noise power ratio (SNR). The computation time needed by the
GS
algorithm for both 2D and 3D localization problems is on the order of seconds. The dual-tag sensor approach is compared to the synthetic aperture radar (SAR) approach. It is shown that the SAR approach yields very good localization accuracies only for 2D localization problems and when SNR is high, but it does not work either for 3D localization problems or for 2D problems with low SNR.
Journal Article
Shape, size, and quantity of ingested external abrasives influence dental microwear texture formation in guinea pigs
Food processing wears down teeth, thus affecting tooth functionality and evolutionary success. Other than intrinsic silica phytoliths, extrinsic mineral dust/grit adhering to plants causes tooth wear in mammalian herbivores. Dental microwear texture analysis (DMTA) is widely applied to infer diet from microscopic dental wear traces. The relationship between external abrasives and dental microwear texture (DMT) formation remains elusive. Feeding experiments with sheep have shown negligible effects of dust-laden grass and browse, suggesting that intrinsic properties of plants are more important. Here, we explore the effect of clay- to sand-sized mineral abrasives (quartz, volcanic ash, loess, kaolin) on DMT in a controlled feeding experiment with guinea pigs. By adding 1, 4, 5, or 8% mineral abrasives to a pelleted base diet, we test for the effect of particle size, shape, and amount on DMT. Wear by fine-grained quartz (>5/<50 μm), loess, and kaolin is not significantly different from the abrasive-free control diet. Fine silt-sized quartz (∼5 μm) results in higher surface anisotropy and lower roughness (polishing effect). Coarse-grained volcanic ash leads to significantly higher complexity, while fine sands (130 to 166 μm) result in significantly higher roughness. Complexity and roughness values exceed those from feeding experiments with guinea pigs who received plants with different phytolith content. Our results highlight that large (>95-μm) external silicate abrasives lead to distinct microscopic wear with higher roughness and complexity than caused bymineral abrasive-free herbivorous diets. Hence, high loads of mineral dust and grit in natural diets might be identified by DMTA, also in the fossil record.
Journal Article
Osteo-pathological analysis provides evidence for a survived historical ship strike in a Southern Hemisphere fin whale (Balaenoptera physalus)
The life history of a fin whale (Balaenoptera physalus) caught during whaling operations in the 1950s was partly reconstructed. 3D surface models of the bones of the skeleton curated at the Zoological Museum of Hamburg were used for an osteopathological analysis. The skeleton revealed multiple healed fractures of ribs and a scapula. Moreover, the processus spinosi of several vertebrae were deformed and arthrosis was found. Together, the pathological findings provide evidence for large blunt trauma and secondary effects arising from it. Reconstruction of the likely cause of events suggests collision with a ship inflicting the fractures and leading to post traumatic posture damage as indicated by skeletal deformations. The injured bones had fully healed before the fin whale was killed by a whaler in the South Atlantic in 1952. This study is the first in-detail reconstruction of a historical whale—ship collision in the Southern Hemisphere, dating back to the 1940s, and the first documentation of a healed scapula fracture in a fin whale. The skeleton provides evidence for survival of a ship strike by a fin whale with severe injuries causing long-term impairment.
Journal Article
Opportunistic Feeding Strategy for the Earliest Old World Hypsodont Equids: Evidence from Stable Isotope and Dental Wear Proxies
The equid Hippotherium primigenium, with moderately hypsodont cheek teeth, rapidly dispersed through Eurasia in the early late Miocene. This dispersal of hipparions into the Old World represents a major faunal event during the Neogene. The reasons for this fast dispersal of H. primigenium within Europe are still unclear. Based on its hypsodonty, a high specialization in grazing is assumed although the feeding ecology of the earliest European hipparionines within a pure C3 plant ecosystem remains to be investigated.
A multi-proxy approach, combining carbon and oxygen isotopes from enamel as well as dental meso- and microwear analyses of cheek teeth, was used to characterize the diet of the earliest European H. primigenium populations from four early Late Miocene localities in Germany (Eppelsheim, Höwenegg), Switzerland (Charmoille), and France (Soblay). Enamel δ(13)C values indicate a pure C3 plant diet with small (<1.4‰) seasonal variations for all four H. primigenium populations. Dental wear and carbon isotope compositions are compatible with dietary differences. Except for the Höwenegg hipparionines, dental microwear data indicate a browse-dominated diet. By contrast, the tooth mesowear patterns of all populations range from low to high abrasion suggesting a wide spectrum of food resources.
Combined dental wear and stable isotope analysis enables refined palaeodietary reconstructions in C3 ecosystems. Different H. primigenium populations in Europe had a large spectrum of feeding habits with a high browsing component. The combination of specialized phenotypes such as hypsodont cheek teeth with a wide spectrum of diet illustrates a new example of the Liem's paradox. This dietary flexibility associated with the capability to exploit abrasive food such as grasses probably contributed to the rapid dispersal of hipparionines from North America into Eurasia and the fast replacement of the brachydont equid Anchitherium by the hypsodont H. primigenium in Europe.
Journal Article
Why ruminating ungulates chew sloppily: Biomechanics discern a phylogenetic pattern
There is considerable debate regarding whether mandibular morphology in ungulates primarily reflects phylogenetic affinities or adaptation to specific diet. In an effort to help resolve this debate, we use three-dimensional finite element analysis (FEA) to assess the biomechanical performance of mandibles in eleven ungulate taxa with well-established but distinct dietary preferences. We found notable differences in the magnitude and the distribution of von Mises stress between Artiodactyla and Perissodactyla, with the latter displaying lower overall stress values. Additionally, within the order Artiodactyla the suborders Ruminantia and Tylopoda showed further distinctive stress patterns. Our data suggest that a strong phylogenetic signal can be detected in biomechanical performance of the ungulate mandible. In general, Perissodactyla have stiffer mandibles than Artiodactyla. This difference is more evident between Perissodactyla and ruminant species. Perissodactyla likely rely more heavily on thoroughly chewing their food upon initial ingestion, which demands higher bite forces and greater stress resistance, while ruminants shift comminution to a later state (rumination) where less mechanical effort is required by the jaw to obtain sufficient disintegration. We therefore suggest that ruminants can afford to chew sloppily regardless of ingesta, while hindgut fermenters cannot. Additionally, our data support a secondary degree of adaptation towards specific diet. We find that mandibular morphologies reflect the masticatory demands of specific ingesta within the orders Artiodactyla and Perissodactyla. Of particular note, stress patterns in the white rhinoceros (C. simum) look more like those of a general grazer than like other rhinoceros' taxa. Similarly, the camelids (Tylopoda) appear to occupy an intermediate position in the stress patterns, which reflects the more ancestral ruminating system of the Tylopoda.
Journal Article